NDLI: Partial Geometric Hashing for Retrieving Similar Interaction Protein Using Profile

Content Provider	IEEE Xplore Digital Library
Author	Kiuchi, Y. Ozaki, T. Ohkawa, T.
Copyright Year	2007
Description	Author affiliation: Graduate Sch. of Sci. & Technol., Kobe Univ. (Kiuchi, Y.; Ozaki, T.; Ohkawa, T.)
Abstract	Protein function is expressed by binding to other compounds at a local portion, called an interaction site. Since the structure of its interaction site and function of a protein are closely related, retrieving similar interaction protein is effective in clarifying the function of a protein. We have proposed a method for retrieving similar interaction protein using profiles that represent the features of the interaction site binding to a certain compound. In this method, it is necessary to compare the structure between proteins and a profile, we use geometric hashing technique which is one of the popular methods for structure comparison. However, the problem of structure comparison by using the geometric hashing is that memory usage becomes too large. This paper proposes a method for arranging the geometric hashing to alleviate this problem. Firstly, only small parts of the target structures are stored in the hash table to reduce the size of the hash table. By evaluating this hash table we screen out candidates of similar structures between target proteins and query profiles. Secondly overall structures are compared for these candidates. In order to reduce the time for retrieval we evaluate the information of the origin which is not generally evaluated without increasing the size of the hash table. Reference set, the basis for transforming in geometric hashing, are sorted
Sponsorship	Premier Hall for Sci. and Eng
Starting Page	589
Ending Page	596
File Size	168105
Page Count	8
File Format	PDF
ISBN	0769527760
DOI	10.1109/ITNG.2007.147
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-04-02
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Solid modeling Amino acids Information retrieval Spatial databases Functional analysis Large-scale systems Chemical compounds Information technology
Content Type	Text
Resource Type	Article

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